


Omeganite

by Alethea12



Category: Shadowhunters (TV)
Genre: Alpha/Beta/Omega Dynamics, Anal Sex, F/M, M/M, Rape, Rape/Non-con Elements, Rough Sex, Suicide, Suicide Attempt
Language: English
Status: In-Progress
Published: 2019-07-05
Updated: 2019-07-05
Packaged: 2020-06-11 18:36:30
Rating: Explicit
Warnings: Graphic Depictions Of Violence, Rape/Non-Con
Chapters: 6
Words: 4,875
Publisher: archiveofourown.org
Story URL: https://archiveofourown.org/works/19546123
Author URL: https://archiveofourown.org/users/Alethea12/pseuds/Alethea12
Summary: This is based in a alpha/beta/omega world.Omeganite: Omega shadowhunters trained for the purpose of pleasing alphas and reproducing. Male shadowhunter omegas have angel wings and are very rare.At the age of 13, Alec never thought that he would be presenting as a omega, and when his father finds out his true gender he gets sent to the omeganite academy. This story is set before Alec meets magnus.





	1. Chapter 1

**Author's Note:**

> Hello this is my first ever fanfic! This story contains many graphic things so please read the tags.
> 
> Alec: 19  
> Izzy: 17  
> Jace: 17  
> Max: 10

Hello everyone,

This is my 1st fanfic, I will most likely delete this once I have the first chapter up. I have a few ideas for this fanfic but beware it will probably be brutal. I hope that you guys still end up enjoying this story. Chapter will be up shortly, since I am new to this site I will be spending some time trying to figure out how everything works.

Thank you.


	2. Alphas

**Notes for the Chapter:**

> This chapter contain non consensual sex and mentions of suicide. If I missed a tag please let me know and I will add it as soon as I can.

When Alec was a child, he never expected to be in this kind of situation. He has seen men and women around the institute, kneeling in front of alphas, being commanded to do things no child should ever see. He never wished it upon anyone for that to happen. But here he was. Sitting on his knees in the assigned omeganite room in the institute, the smell of sex, blood, pain and arousal prominant. There are 5 beds in this room as each institute is given 5 omeganites, they were down to 4 at the New York institute since the last one couldnt handle it and took her own life.

On his left there is a female omeganite with a shadowhunter that came in from the clave a couple of hours ago, he never bothers to learn their names. The alpha commanded her to ride him, his hands gripping her thighs while he chases his own release. On his right he sees Andrew Underhill, omeganite, his hands are chained to the metal headboard on the uncomfortable bare bed, his wings are out, the outside of the feathers a bright white color with the center of them being a light brown. The swirls of the omeganite brand showing clearly on his left hip glows a angry red color as he tries to fight off a order his current alpha commanded. He will be punished for that later. Male omegas always get it worse as there is less then 100 of them left in the world.

Alec hears the door open and immediately bows his head, his hands are placed neatly on his lap clasped together, he is kneeling on the hard tile floor, the only thing covering him are his black boxers per his current alphas request. His scars show up easily on his pale skin, most of his body is covered by them, from punishments, from his alphas, some were made by himself a year ago when he couldnt take the pain anymore. His alphas name is Sebastian Verlac, when he first met him he seemed sweet, but those are the ones you have to be careful of. He was one of the worst alphas he has had to serve, and he has had many.

Sebastian walks up to Alec, his green eyes raking over Alec. He grabs Alec by the hair.  
"Did you miss me, omega?" He asks while pulling so hard on his hair that Alecs ocean blue eyes start to water.

"Yes alpha" he replies back.

Sebastian pulls Alec in a position where he is bent over the foot of the bed and commands him not to move.

"I have had a very hard day today because of you. Everything is your fault" Everything is always Alecs fault according to Sebastian.

Alec bites his tongue to prevent himself from talking back, Sebastian hates it when he speaks without permission.

All of a sudden Sebastians phone starts to ring, he is needed in the training room.

"Dont think you're getting out of this, I still have time to fuck you omeganite."

In one swift movement Alecs boxers are torn to shreds, he hears the zipper from Sebastians pants being pulled down and takes a deep breath trying to prepare himself for what's to come. 

Sebastian pushes himself in Alec with one hard thrust, he screams out in pain. He never can get used to this kind of pain no matter how often it happens. Sebastian keeps thrusting into Alec, groaning, Alec begs him to stop as the pain gets more and more unbearable as his knot starts to form inside of him. Sebastian pulls Alecs hair and uses it as leverage to push himself deeper, his other hand on his hip, it will leave new bruises later. He pulls out right before climaxing and ejaculates all over Alecs back as he didnt have time to properly knot him.

Alec could feel the warm blood dripping down his thighs and tries not to think too much of what just happened, he thinks about his siblings, about a time before he was used as a whore for the clave, a time where he was allowed to be happy and not used by half of the alphas in new york.

Sebastian dresses himself and leaves but not before promising that he will be back that night. As soon as he leaves the room the command is lifted and Alec can move once again. It is now 6am and time to get ready for the day. He is a omeganite whore by night, shadowhunter by day and wishes that one day someone will save him from this horror movie he calls his life.


	3. Missing downworlders

Alec makes his way to his room, applies a iratze, showers and dresses in his regular black shadowhunter clothing topped off with a black leather jacket. He can usually do as he pleases during the day as long that he follows his alphas rules.

He heads to the cafeteria to meet his siblings for breakfast, luckily for them Izzy and Jace both turned out to be alphas. They know what happens to him but found out very early on that they cant do anything about it as it results in their brother getting more injured.

"Hey Alec! I saved you some bacon" Said Izzy

"Thanks Iz, I hate it when they run out. Anything happen last night while I was out?"

"There has been news of some attacks against some downworlders, weve been looking for some sort of pattern to figure out what is causing this but we havnt come up with anything." Says Jace

"This is what, the 4th attack against downworlders this month?" Asks Alec

"According to Meliorn a seelie has gone missing so it might be the 5th" Says Isabelle

"Ok let's meet up in the weapons room in a hour to go over all of the details" Says Alec

\-------------------------------------------------------------------

"So far 2 warlocks, 3 werewolfs, 1 vampire, and 1 seelie have gone missing. There were no witnesses left alive, no clues or evidence have been found" states Isabelle

Alec looks at the pictures of the crime scenes, bodies spread out across the pictures.

"Did they find out how they died?" He asks

"They bled to death by cuts, we cant identify the weapon as there are no actual stab wounds though the wounds did have a poison in them to prevent the wounds from healing." Says Isabelle

"Alright let's check out the latest scene, maybe I can pick up something that everyone else missed." Says Alec

As a male omega, Alecs sense of smell has always been stronger then the others, he also wields some of the Angel's powers though he hasnt been able to practise them very much as it is illegal for a omeganite to practise their magic.

Alec was so caught up in the mission that he forgot to inform his alpha that he was leaving the institute, according to alphas, omegas are the weakest of their race due to them being smaller then them and a omeganites alpha has to approve of everything that they do. An omeganites job afterall is to carry pups and please their alphas, and nothing boosts an alphas ego more then being able to control what he does.

Right before stepping out of the institute Alec realizes his mistake when his face makes contact with the cement wall.

"Where do you think you're going omeganite?" Sebastian growls out in his ear while tightening his hold

Both of his siblings growl at Sebastian from the doorway. He will pay for that later.

"I'm sorry alpha, I have been tasked with the missing downworlders mission and was going to examine the crime scene. Please forgive me alpha, I was being selfish in not telling you my whereabouts." Said Alec, his lip now cut and steadily bleeding down his shirt. He can also feel a bruise forming on his cheek.

"Selfish omeganite. You have 1 hour and you better be back here or you wont be allowed to leave this institute for the next month." Said Sebastian while inhaling his scent. "And dont even think of fucking other alphas while you're out, you belong to me."

"Yes alpha" said Alec and he was released from the hold.

Alec knows Sebastian is serious. He has always fully carried out his threats. He was once locked in his room for 2 weeks for being late to a meeting with his alpha. He was only allowed to eat once a day and had to stay kneeled at the end of the bed the entire time, his knees hurt just thinking about it.

Alec and his siblings walk for a couple of blocks before Jace interrupts his thoughts.

"I dont know how you deal with him, it kills me not being able to do anything and having to just stand by and watch. You're so much stronger then him Alec! You win while sparring with me all of the time, how can you let him treat you like this?"

"I dont have a choice Jace. This omeganite rune controls my life, fighting isnt worth it anymore. You know the only way to cancel out the rune is to be truly mated and it will never happen for me." Said Alec

"The hell it wont!" Screamed Isabelle "You're amazing big brother, anyone would be lucky to have you as their forever mate."

Alec gave Isabelle a little smile "Thanks Iz but we both know that it's extremely rare a omeganite gets mated"

The 3 went silent again until they made their way to the latest crime scene. It was a back ally near a popular stretch of bars. Alec took a deep breath and inhaled the smell of alcohol and cigarettes. He focused more and breathed in again, he can smell blood, he can sense the fear of the seelie, he can smell hints of love, he senses anger. The seelie that was murdered here was the mate of the one that was taken, he can now tell that one was a omega, the other a alpha.

"Iz, were all the ones taken mated omegas?" Asked Alec

"Not all of them, one of the warlocks were an alpha, and a werewolf was a beta" She replied

Most of the blood was cleaned away from the ally but Alec was able to smell it extremely concentrated, he followed the smell to a dumpster.

Jace activated his strength rune and pulls out the dumpster. All 3 stare dumbfoundly at what they find underneath.

A seraph blade covered in seelie blood.

**Notes for the Chapter:**

> Thank you all for reading! 
> 
> This story will be updated slowly as I type as I go when I have the time. This is also my first story ever written but I will try my best to finish it off.
> 
> You guys are amazing!


	4. Fingerprints

**Notes for the Chapter:**

> I am so sorry it has taken this long to update! I am in the process of buying a house and let me tell you, it's a lot of work! I hope you enjoy!

They return to the institute with 10 minutes to spare and start writing out their reports of the crime scene. Isabelle takes the blade to further examine it to hopefully find out who it belongs to. 

"This doesn't make any sense, how can a shadowhunter do this to them? Where are they putting the missing downworlders?" Asks Iz

"Honestly I'm not surprised, the things they do to their own kind because of our genders is bad enough, who knows what they've been doing to them." Replies Alec "I have to find Sebastien so he knows that I'm here on time."

"Keep us updated if you find anything on that blade" says Jace before they all split ways.

Alec walks around the institute searching for his alpha but comes up empty, when he reaches the head institutes office he finds out why.

"Maryse, Robert, what are you doing here? You aren't due for a couple more weeks" says Alec while kneeling on the ground near the entrance. Alec has had a terrible relationship with his parents since he presented, his father is the reason he is a omeganite today and his mother stood by and did nothing to stop his father.

They were expecting their eldest son to be a alpha as no omegas run in their family, saying they were disappointed would be a understatement.

"You are failing this family's honor Alec, you are supposed to protect this city even for the pesky downworlders but we keep receiving reports of them missing and dead, the clave has been receiving death threats! We're here to do damage control."

"Oh please, the last I heard I wasnt your son anymore Robert. I am doing the best I can with all these limitations you have put on me with being a omeganite, how am I supposed to get any work done as temporary head when omeganites cant even speak without permission from their alphas"

Smack!

Alec goes flying across the floor, a large red handprint across his face. He gets back on his knees.

"Is that all you got Robert? I have dealt with much worse then you." Alec says leveling his blue eyes with his father's brown ones.

Crash!

Alec went flying into a small table breaking a vase that was on it. He clutches his side where his father kicked him and spots some blood from a piece of glass in his hand.

"Have you forgotten all your training boy? Shall I make you a appointment for re education?"

Alec freezes, blue eyes wide open with fear clearly showing on his face. From what he has heard, re education is worse then the first time in the omeganite academy. Those who go there never come back the same.

"Enough!" Maryse yells. "We are here for buisness. Clean yourself up and update us on the case. You have 20 minutes, be quick. Also your alpha will be away for the next 2 days, you will answer to us until then. Do I make myself clear?"

"Yes alpha" alec replies, his voice barely a whisper.

"Speak up, so pathetic. Be a good boy and clean up this mess before you go" Robert replies.

"Yes Alpha! Of course, I understand alpha."

\------------------20min later---------------

Alec returns to the office, bruise starting to form on his face. Since his parents are his current alphas he knows the drill, no healing runes allowed unless he's on the verge of death. It's how Robert likes it.

Isabelle is also in the office sitting on a chair, Alec kneels on the hard floor beside her taking his usual position, head down, hands behind his back. The room is quiet for a few minutes until Jace walks in disturbing the silence.

"Did you find anything on the blade?" Asks Jace

"What blade?" Asks Maryse "Speak Alec"

"Earlier today we examined a crime scene and discovered a seraph blade covered in blood, Isabelle was in charge of examining the blade, alpha." Replied Alec

"What did you find?" Demanded Robert

"I found 2 fingerprints on the knife... The odd part though is that the fingerprints... the person is supposed to be dead." Replied Isabelle

"Spit is out already Isabelle." Said Robert

Isabelle glared at her father, if she had any powers he would be buried 500 feet under the ground with that look. Robert broke her gaze and muttered something ineligible. Alec may have no choice but to obey but Isabelle is a strong alpha and knows how to hold her own ground.

"They belong to Valentine Morgenstern."


	5. Step one

**Summary for the Chapter:**

> This chapter contains graphic rape and many other abuses and tortures like the previous chapters so far. You have been warned.

**Notes for the Chapter:**

> Sorry that I haven't posted in a while! I still plan on finishing this story, I have just been extremely busy lately. But fear not I will not abandon you guys or this story.
> 
> Leave comments! I love reading what you think of my very twisted story.
> 
> Thanks for reading

Missing downworlers. Valentine. All the dots finally connected.

The first time around Valentine had tried to steal the mortal cup to make new shadowhunters but he had never gotten the chance. While he was waiting for the perfect timing to get the cup he would kill downworlders and do experiments on them while forcing omegas to carry pups. 

Valentine is the reason that omeganites exist in the first place. He had convinced the clave that our numbers were low and since omegas get pregnant easily he focused on them. Omegas were once respected warriors, because of their wings, instincts and powers they were nearly unstoppable in battle. Shadowhunters were a force to be reconned with, with the omegas in the air and the others fighting on the ground they were nearly unstoppable. But Valentine won his arguments and created a new law, the omeganite law, and a new rune that inflicts immense pain to omeganites who deny orders.

And he was alive.

After the meeting with his parents Alec barely remembers sending documents to the clave, updating schedules and doubling patrols. He gets permission from his mother to head to bed early that night, normally he is allowed 4 hours of sleep if he is good and because he had found the seraph blade his mother allowed him 6 hours of much needed rest.

Unfortunately he is too used to his schedule and only manages to sleep 5 hours. He decides to go to the training area to practise with his bow and arrow.

Alec stands far from the targets and let's his arrows fly. Arrow after arrow hits the target and his mind goes back to before he presented as a omega.

\------------Flashback age 11 --------------

3 arrows fly into their respective targets, perfect shots.

"Wow great job son! You are a very quick learner. You make me very proud." Says Robert while patting his son on the shoulders. "You will make a great alpha and our family honorable again" he continues

"Thanks dad" Alec replies with a smile "I need to work a bit on shooting my arrows quicker but I wont let you down."

"I know you won't Alexander" he replies "Dont forget to eat breakfast, I'll have them make extra bacon for you" he says and leaves the room.

Alec heads to his room first to clean up before going to the cafeteria, when he enters he finds his sister crying. Alec runs up to her and checks her for any wounds, she looks ok. "What's wrong Iz?" He asks

"I'm in so much trouble big brother" she says while holding out mothers favorite vase 

Alecs blue eyes widen in fear before he puts on his mask and takes the vase. "Its going to be ok Iz, I'll fix it and they wont even know it broke"

"You're the best brother ever" she replies and hugs Alec

Before Alec has the chance to fix the vase his father bursts into his room "Alec have you seen Max? He wont stop crawl... Is that your mothers vase?!?" Robert yells out while taking it out of Alecs hands

Isabelle begins to cry harder and his father sets his glare on her but before she says anything Alec speaks up

"I'm sorry dad, I tripped and it fell to the ground. It was all my fault."

His glare turned back to Alec

"Isabelle, go to the cafeteria and eat breakfast" he says in a calm manner. Alec tenses up but tries not to show his unease as Isabelle leaves the room. The silence in the room is now unbearable, Alec can hear every tick on his father's watch as minutes go by, he knows he will be punished but he is used to taking the punishments for his siblings by now.

"25 lashes since you were good up to this point. No more extra bacon today. You will care for Max for the next 3 days. And you will glue every piece of this vase back together."

"Yes sir" Alec replies as he turns around, takes off his shirt and leans forward against his desk. He already has 5 silver scars running down his back from a very bad previous lashing he received. He refuses to yell out with every lash, he fights off his instincts and his father, he will do anything to protect his siblings. He will not fail.

\-------End of flashback -------

The times were nice back then, even with the occasional lashings he still had more freedom then anyone can ever ask for and was well respected, he was set to be the next head of the institute. He wasn't always this willing to do what he is forced to do daily, even to this day no one has been able to truly break him, he has learned which fights are winnable and which are impossible to win.

One more arrow flies into the target before Underhill walks in to tell him it's their turn in the omeganite room. Even with his alpha out of town he had to serve others. Alec and Andrew are good friends, almost family with everything they've had to endure together.

Once they reach the room they strip and kneel by the beds while they wait for alphas to come in, Alec fills in Andrew on Valentine as he had been busy when the announcement went through. 

"Alec, are we in danger of Valentine? Last I remember hearing he liked to breed our kind, I don't know how much more I can take" says Andrew

"I'm really not sure, we will have to just stick together and we will get through this. He won't be able to take all of us on" replied Alec quietly

The door opens and 2 alphas come in "here we go again" whispers Alec as he turns off his mind and prepares himself mentally for what he has to do.

Alec recognizes the man he is partnered with, he wishes it was someone who took him rough, instead he likes pleasing Alec. Alec has no choice but to put on a show for him as if he does bad with this alpha it will be reported to his and he will be punished once again.

Alec kisses the shadowhunter and runs his hand in his brown hair. Alec kisses his way down the man's body and takes his member into his mouth. He has done this what felt like thousands of times, they train you to do this in the omeganite academy so he is used to it.

The man pulls Alec off after a few minutes and grabs Alecs member, he turns Alec around and pushes him over the bed while still stroking him. His member starts hardening and he feels betrayed by his body. This felt like the worst type of torture to Alec, he would rather feel only pain then pleasure. The man moans behind Alec and slowly pushes himself inside of him without preparation. Alec yells out in pain until he adjusts. The man pumps his hand faster while he begins moving inside of Alec, they both let out a moan and Alec feels ashamed. The man continues on until they both reach a climax and Alec is knotted. He used to get worried of getting pregnant, he had become pregnant 3 times before, but lately he has been so malnourished that he knows his body wont support a child.

He lays there squished into the mattress with this sweaty man laying across his back. He looks over and sees Andrew doing the same thing he had just done with his alpha. He hates his life. He doesn't want to live this way anymore. He needs to find his soulmate to break this rune. So while he's laying underneath this stranger with cum and blood running down his legs, he makes himself a promise that he will be free again one day and will make changes in this world. He wants to build a world where no one else has to suffer like this.

Step one is defeating Valentine once and for all.


	6. Golden eyes

Pandemonium. What is it you may ask? It's a club for all, downworlders, humans, shadowhunters, alpha, beta, omega. All are accepted, so of course that's the best place to go looking for information about Valentine.

Jace and Isabelle are very familiar with the place, Alec has only been on the outside to drag one or both of his siblings back to the institute after they've drank too much.

There is a long line outside of the club but they cut straight to the front but not without many complaints, the doorman recognizes them right away and let's them in, a bonus of his siblings frequenting the establishment so much.

The music is so loud Alec can feel the vibrations through the floor, the club is crowded with people, some are dancing, drinking, talking, while others are in much more compromising situations, they should atleast take advantage of the private rooms Alec thinks. Alec hates big crowds, it gives him very bad anxiety.

"Hey I'm going to get a drink and see if I can find anything out!" Isabelle yells out before taking off towards the bar

"Me too! I think I made out with that girl last week" says Jace, before he can take off Alec grabs his arm and stops him

"You cant leave me alone here Jace, I hate crowds and you know I get a lot of unwanted attention when I'm alone" says Alec

Jace gives him a sympathetic look and throws his arm around Alecs shoulders

"You know what brother? Maybe you will meet your soulmate tonight! There is so much potential! What do you think of that guy over there? Possible soulmate?"

Alec surpresses a cringe when he spots the man, he is a bald white human man, 5'5, slightly overweight, clearly in his 40s and definitely not his type.

"You know what, I think I'll be ok on my own" Alec tells Jace

As Jace wanders off Alec decides to wander around the club, he is amazed at what he sees. Everyone in here is being treated as an equal, everyone is laughing, dancing, kissing and having a lot of fun, nothing against their will. He yearns to feel that way, to feel free and happy. One day he tells himself. He walks by a long hallway with many doors, he peaks into one and sees two women, naked in a very compromising situation. Both women look at him and giggle "would you like to join us?" One asks while the girl kisses down the others neck

"Sorry I didn't mean to interrupt you, I'll go now" Alec replies feeling slightly uncomfortable. He doesnt have anything against women but he definitely is not interested in anything more then friendship with them.

He wanders a little deeper down the hallway when he hears a small scream, the music is so loud he can't pinpoint where it came from. Alec closes his eyes, takes a deep breath and let's go of his sense, his eyes turn golden underneath his eyelids, his teeth sharpen to small points and his energy seeks out for any possible danger. He follows his gut that leads him to the last room on the left side of the hallway.

Alec hears a little scuffle on the other side of the door and presses his ear to it to avoid another situation like before "please stop, dont do this!" He hears a girl cry out, he immediately breaks down the door and asseses the situation.

The girl, a warlock Alec notices by her purple skin, is pinned on the ground with her clothes torn off, her face bleeding heavily, and on top of her is a man, a shadowhunter, with a bright red circle ruin burned into his neck.

"Stop screaming you little bitch, you're exactly where a dirty warlock deserves to be" the circle member says while attempting to push himself into her

Alec kicks the man in the abdomen so hard he goes flying into the wall. The girl runs out of the room crying as soon as she is free and Alec turns his anger towards the circle member. Before he can stand up Alec is on him, he holds him by the throat and repeatedly hits him in the face. The man knees Alec in the side and he stumbles back but it's not enough to stop Alec. Alec blocks the man's next attack and twists his arm behind his back and pulls up until he hears a crack, this circle member is terribly trained Alec notices as he cries out in pain. Alec pushes him to the floor and holds him down when multiple people flood the room.

He finally tears his golden eyes away from him to examine the situation, the girl now wrapped in a robe has tear streaks and blood going down her face, beside her is a vampire man that Alec recognizes as the head of the vampire clan, his siblings are also there along with a man. He has never seen anyone like him before, his olive colored skin, soft lips, tall stature, muscles peaking from his half open shirt, Alec meets the man's cat eyes and he stops breathing. His eyes glow brighter, his ruins turn from black to gold and his back tingles from his wings trying to emerge. Everyone's eyes go wide and Alec feels very very trapped, his chest is tightening and it's getting very difficult to breathe. He looks around the room for a escape but the door is the only way in or out, it's too much, Alec faints.


End file.
